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Crystal structure of the F87M/L110M mutant of human transthyretin at pH 4.6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F41 1F41 POLY ALA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 ZINC ACETATE 0.2 M, SODIUM CITRATE 0.1 M, AMMONIUM SULFATE 2,0M, PH 4,6; CRYSTALS WERE SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 10 % GLYCEROL BEFORE FREEZING IN LIQUID NITROGEN, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 4.60
Crystal Properties Matthews coefficient Solvent content 2.15 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.95 α = 90 b = 60.69 β = 89.98 c = 82.99 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2008-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.3050 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.383 83.045 97 0.056 0.056 7.1 7.1 92482 92482
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.383 1.46 94.7 0.774 0.774 1 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1F41 POLY ALA 1.383 19.37 92482 92475 5424 97.2 0.159 0.157 0.1794 0.202 0.1931 RANDOM 25.11
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.37 -0.07 0.35 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.002 r_dihedral_angle_3_deg 16.242 r_sphericity_free 14.649 r_dihedral_angle_4_deg 11.985 r_sphericity_bonded 9.161 r_dihedral_angle_1_deg 8.125 r_scangle_it 7.417 r_scbond_it 5.712 r_mcangle_it 4.416 r_rigid_bond_restr 3.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.002 r_dihedral_angle_3_deg 16.242 r_sphericity_free 14.649 r_dihedral_angle_4_deg 11.985 r_sphericity_bonded 9.161 r_dihedral_angle_1_deg 8.125 r_scangle_it 7.417 r_scbond_it 5.712 r_mcangle_it 4.416 r_rigid_bond_restr 3.817 r_mcbond_it 3.375 r_angle_refined_deg 2.633 r_symmetry_hbond_refined 0.466 r_symmetry_vdw_refined 0.392 r_nbtor_refined 0.33 r_chiral_restr 0.311 r_nbd_refined 0.292 r_xyhbond_nbd_refined 0.258 r_symmetry_metal_ion_refined 0.243 r_metal_ion_refined 0.123 r_bond_refined_d 0.03 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3558 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 81
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling